galaxyproject/tools-devteam — pull request #20 by jmchilton (2014-11-11 21:09:44+00:00)
Title: Enhance cufflinks for Dataset Collections

![Enable workflows over many replicates](http://i.imgur.com/Ce8zcsG.png)

- Use multi-data input in several spots instead of repeats. (Currently downside of multiple inputs versus repeats is that they don't allow duplicate inputs via UI (API allows it) - is there ever any reason for these inputs to pass same file twice?).
- Updated cuffdiff/cuffnorm for even more sophisticated potential collection use cases if conditions are identifiers to 1-D `list` of samples or 2-D list (`list:list`) with many samples per condition.